A simple demo that fetches a protein sequence from the UniProt web site, submits it to the Hmmer3 service and prints the results.

```java /*

* @since 3.0.3
*/
   public static void main(String[] args){

       try {
           // first we get a UniProt sequence
           String uniProtID = "P26663";
           ProteinSequence seq = getUniprot(uniProtID);

           // now we submit this sequence to the Hmmer web site
           HmmerScan hmmer = new RemoteHmmerScan();

           SortedSet` results = hmmer.scan(seq);`

           // let's print the obtained annotations
           
           System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
                   "Domain","ACC", "Start","End","eValue","Description"));
           
           int counter = 0;
           for (HmmerResult hmmerResult : results) {
               //System.out.println(hmmerResult);

               for ( HmmerDomain domain : hmmerResult.getDomains()) {
                   counter++;
                   System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
                           counter,
                           hmmerResult.getName(), domain.getHmmAcc(), 
                           domain.getSqFrom(),domain.getSqTo(),
                           hmmerResult.getEvalue(), hmmerResult.getDesc()
                           ));

               }

           }

       } catch (Exception e) {
           // TODO Auto-generated catch block
           e.printStackTrace();
       }
   }

   /** Fetch a protein sequence from the UniProt web site
    * 
    * @param uniProtID
    * @return a Protein Sequence
    * @throws Exception
    */
   private static ProteinSequence getUniprot(String uniProtID) throws Exception {
       
       AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
       UniprotProxySequenceReader` uniprotSequence = new UniprotProxySequenceReader``(uniProtID,set);` `       ` `       ProteinSequence seq = new ProteinSequence(uniprotSequence);` `       ` `       return seq;` `   }`

```

This will create this output:

#            Domain        ACC  Start   End   eValue    Description
1        HCV_capsid PF01543.11      2     115   0.00e+00    Hepatitis C virus capsid protein
2          HCV_core PF01542.12    116     190   1.09e-43    Hepatitis C virus core protein
3           HCV_env PF01539.11    193     382   0.00e+00    Hepatitis C virus envelope glycoprotein E1
4           HCV_NS1 PF01560.11    386     729   0.00e+00    Hepatitis C virus non-structural protein E2/NS1
5           HCV_NS2  PF01538.1    811    1005   0.00e+00    Hepatitis C virus non-structural protein NS2
6     Peptidase_S29  PF02907.9   1056    1203   0.00e+00    Hepatitis C virus NS3 protease
7        Flavi_DEAD  PF07652.8   1294    1355   8.20e-06    Flavivirus DEAD domain
8          HCV_NS4a PF01006.14   1658    1711   7.20e-25    Hepatitis C virus non-structural protein NS4a
9          HCV_NS4b PF01001.13   1728    1921   0.00e+00    Hepatitis C virus non-structural protein NS4b
10         HCV_NS5a PF01506.13   1974    1996   2.10e-10    Hepatitis C virus non-structural 5a protein membrane anchor
11      HCV_NS5a_1a  PF08300.7   2006    2067   1.40e-34    Hepatitis C virus non-structural 5a zinc finger domain
12      HCV_NS5a_1b  PF08301.7   2068    2168   2.80e-45    Hepatitis C virus non-structural 5a domain 1b
13       HCV_NS5a_C  PF12941.1   2179    2419   0.00e+00    HCV NS5a protein C-terminal region
14           RdRP_3 PF00998.17   2422    2932   0.00e+00    Viral RNA dependent RNA polymerase